Before you interview custom builders, you'll need a set of working plans called builder's plans from your architect. As this video explains, choosing your builder comes down to a mix of who has the experience required for your project and with whose personality you mesh well.
After checking the licenses and reputation of a few builders, interview the top two to three builders.
You'll need to ask questions that let you get to know their past projects and preferred forms of communication. The latter matters because you'll need to contact your builder with questions and updates. If they love to talk on the phone, but you prefer texting and email so you can refer back to information later, you need to know that they'll make an exception for you, not expect you to cater to them.
Inquire about how flexible of a building process they provide. How late in the process can you change materials or choose a design option?
You'll also need to find out from each builder the time required for them to build a home and whether they provide a warranty on their work. Does that warranty extend to subcontractors they may use?
Your custom builder creates your dream home. Choose them wisely.